The Barriers That Divide our Hearts
by Shin-man
Summary: Another take on the life of Shinji Ikari, and the "what ifs" that could happen. Shinji receives help from someone that understands him more than he knows, and in the process becomes something more. This is a Misato/Shinji fic because there is no better pairing.
1. Chapter 1

Well here is the first chapter. I suddenly got inspiration to write a new fic after watching most of 3.0. This story will take some of the ideas and concepts from the new movie in later chapters so I guess this is a spoiler alert heads up. I don't really have anything else so read and enjoy.

Thanks to Mazoku-sempai for the beta!

* * *

Shinji sat staring at the ceiling listening to his SDAT player while he contemplated the events of the previous day. He had no idea how his life had changed so quickly and so drastically. Just a few days ago he had been living with his uncle going through his boring daily routine. Now he was piloting a giant robot and fighting monsters that came from who knew where.

Rolling over, he faced the wall letting out a large sigh while doing so. How did anyone expect him to get back into that beast? He was just a giant coward. Had his father not tried to force that injured blue haired girl to pilot he probably would have just run like always.

Before his thoughts could continue down the dark road that they were on, he heard a soft knock against his bedroom door. Not wanting to confront his guardian just yet, he paused his music and shut his eyes tightly hoping she would just go away. Sadly for him his wishes went unanswered that night. He heard his bedroom door open slowly with a slight squeak. There was a moment of silence afterwards that seemed to last forever before his guardian spoke.

"Shinji, its Misato. Are you awake?" his purple haired guardian asked.

Shinji continued to lie on his bed with his eyes closed, pretending that he could not hear his new guardian. While he appreciated her kindness to take him in, he couldn't help but feel that she took him in for her own motives and not because she wanted him there.

"Shinji, I just want you to know that you did a very brave thing, and you saved a lot of people because of it. I just wanted to tell you how proud I am of you." Misato spoke to him as if she knew that he was awake. She hesitating slightly before saying, "Good night Shinji-kun. I will see you in the morning." And with that she quietly shut his door.

Waiting several minutes after his door shut Shinji finally rolled back over onto his back to continue staring at the ceiling that was slowly starting to become familiar to him. "How can she be proud of me?" he mumbled to himself. "I don't even know what I did." He sighed again, a bit longer and more drawn out this time. Placing his arm across his eyes to block out his inspection of the white ceiling, a wisp of a smile crossed his face. "Although it is nice to hear that someone is proud of me. I can't remember the last time someone said that to me," he whispered to himself.

As he slowly drifted off to sleep, glimpses of yesterday's battle flashed through his mind. The images made it hard for him to fully fall asleep, causing him to shift back and forth restlessly in his bed. Soon though his terrible visions were replaced with the image of a purple haired woman giving him a warm smile, her mouth moving saying something he couldn't quiet hear.

* * *

The next morning Shinji woke feeling more rested then he thought he would. Swinging his legs out of his bed he slowly rubbed the sleep out of his eyes. He walked over to his closet and pulled out his normal black slacks and white button up shirt. As he dressed, he tried to remember what he dreamed about during the night. All he could remember was the color purple and a feeling of warmth.

"That can't be right," he said to himself. "The only purple thing I can think of is that… beast."

Deciding to just forget about it he opened the door to his bedroom and stepped out into the dimly lit hallway. He made his way toward the kitchen briefly, stopping at Misato's bedroom door. Listening carefully he could hear her snoring loudly through the thin door. Smiling slightly he continued on his way to the kitchen.

"I guess she isn't much of a morning person," Shinji chuckled to himself. "Maybe I should make her something nice for breakfast to say thanks for giving me a place to stay," he said while tapping his chin.

Pulling a pot and skillet out of the cabinets, he grabbed several ingredients and set to work. Soon the whole apartment was filled with the smell of delicious food stuffs. Shinji hummed a classical tune to himself as he cooked; to him the kitchen was the most comfortable place he could ever be. When he cooked he forgot about all the troubles he had. Everything just melted away. As he continued to fry up some eggs he failed to notice someone sneaking up on him.

* * *

The first thing Misato noticed as she started to wake up was that something smelled amazing. That in itself was pretty unusual for her apartment considering most of her meals consisted of the instant variety. After what felt like an eternity she finally managed to detangle herself from her blankets. Sitting up on her futon, she scratched her stomach while trying to suppress a large yawn. Finally managing to stand up she went to her dresser to pick up her yellow tank top from where she had thrown it last night.

After she put on her tank top she studied her reflection in the mirror above her dresser. The years had been kind to her she decided after a few moments. Even though she was nearing 30 years old she still looked much younger than that.

"Small miracles I guess considering the way I eat and drink," she said to the reflection in the mirror.

The delicious smell filled her nostrils once again. She turned away from her dresser and made her way to the kitchen. When she arrived the sight before her was not exactly what she expected. Standing in front of the stove was Shinji; frying something up in the skillet that she couldn't see, but the smell of it left her drooling. This was the most relaxed she had seen him since she had met him, he looked almost normal. A devious smile formed on her face as an idea came to mind. Sneaking up quietly behind the teen she heard him humming to himself.

'_Oh this is gonna be good!_' Misato thought to herself as she prepared herself for a sneak attack. With one final step she launched herself at her unsuspecting prey with a loud yell. "Good morning Shinji-kun!"

* * *

"Good morning Shinji-kun!" was the only thing Shinji heard before his sides were mercilessly attacked by Misato. Shinji began to flail about wildly as the woman continued to tickle, making him lose his grip on the spatula and almost burn himself on the stove at the same time. After a few moments of being attacked, Shinji managed to extract himself from Misato's grasp.

"Misato-san? Wh-what are you doing?" he asked, his face slightly flushed from the tickle attack.

"Aww Shinji-kun you don't have to be that formal with me. It makes me feel old," Misato teased.

"Sorry," Shinji apologized while looking away.

Misato took a step back from the young teen finally giving him some room to move. "It's okay Shinji-kun you don't have to apologize. I was just having a bit of fun."

Shinji turned his eyes back to Misato and the words he was about to speak died in his throat when he looked into her eyes for the first time. She had brown eyes like most others of Japanese descent, but hers were the color of chocolate. They were dark and rich, like deep pools pulling him in leaving no room for escape. He realized for the first time that he had no idea how old she was. She was older than him for sure, but by how much he didn't know. The way she acted from what little interaction he had with her so far she could pass as a teenager. His thoughts were cut short by a loud cough from Misato. Shinji's face turned beat red knowing he had been caught staring.

"Well well Shinji-kun, see something you like?" Misato said with a devilish grin on her face.

"Ahh, uhh, I was just…I'm sorry Misato-san," he replied turning his gaze down in shame.

Misato was slightly taken aback. "Shinji-kun its fine. You aren't the first guy I caught staring at my chest and I doubt you will be the last."

If it was even possible his face became five shades brighter, "I-I wasn't looking… down there!"

Misato smirked, "Well if you weren't looking at my assets," she emphasized this by hugging herself causing her cleavage to press together, "Then what were you looking at?"

"I was uh, looking at your… eyes," responded Shinji, his eyes never leaving the ground.

"What was that Shinji-kun I couldn't hear you?"

"I said your eyes! I was looking at your eyes. I think they are very pretty." He practically shouted visibly shrinking back after doing so.

Misato was really taken back this time, not only because of his outburst but also because of his object of interest or in this case objects. She was no stranger to men ogling her, and she had her fair share of them trying to cop a feel as well. Over the years she had gotten used to the attention that her body brought her, and in some cases put her close quarter combat training to good use. But she could not recall a single instance where anyone said that she had pretty eyes.

"Wow Shinji-kun you are just quite the young gentleman aren't you?" Misato said with a small smile on her face.

Shinji's head snapped up at that comment, his mouth hanging wide. "I, uh… What?" he finished lamely.

Misato chuckled lightly. "Shinji-kun I'm no stranger of men staring at me for all the wrong reasons, but I don't think I have ever caught one staring at my eyes. It's very… endearing."

"Uhh, thanks?"

"I think you and I are going to get along really well Shinji-kun, but I think whatever you were cooking is starting to burn."

Shinji quickly turned around and began frantically trying to save breakfast. Misato made her way to the table and sat down, cracking open a beer that she had grabbed along the way. She watched as her ward attempted to salvage what was left his cooking. A frown crossed her face as she thought back to what she read in his psychology profile. Shy and introverted were the least of his problems, his lack of confidence and confrontation avoidance were much bigger issues in her mind. He was a pilot first and foremost and sending him into battle as is was just asking for trouble. Sighing mentally, she turned her gaze down to the cold drink in her hand.

'_Maybe I should set up a training regimen for him, and take him to the shooting range so he can get some more hands on experience and not just have him work in a simulator,_' she thought to herself. '_That means I will have to start exercising as well.' _She grimaced at the thought, but looked down and pinched her stomach._ 'I could really use it though; years of eating instant meals are starting to take their toll._'

Her inner thoughts were interrupted by Shinji placing a plate of food in front of her on the table. She looked up to see him still standing there looking at her expectantly waiting for her to try his cooking. She picked up her chopsticks and then looked at what he cooked for her. It was a simple dish, a bowl of rice and some fried fish with a small side of miso soup. The smell was heaven to her nose, for something so basic it smelled delicious. Not one for manners she began to inhale the food wondering if his cooking really tasted that good or if she had just been too long without a real meal.

"Mmm Shinji-kun this is delicious, where did you learn to cook so well?" Misato asked between mouthfuls of food.

The teen looked away from his guardian, "Well my uncle was never really around, so I guess I just learned how to cook for myself." He glanced sidelong at her noticing the small frown on her face. "I'm glad you like it though, it's the least I could do for you since you gave me a place to live."

"It's my pleasure Shinji-kun. I don't think I would be able to live with myself if I let you stay in one of those stuffy barracks at headquarters."

"I don't think it could be that bad, and like I said I'm used to being alone so it wouldn't have been much different than before coming here." Shinji replied.

Misato finished what was left of her meal and then stood up to face Shinji. She smiled, trying to make him feel a little at ease. "Well you are stuck with me now whether you like it or not." Tapping him lightly on his nose with her finger she took great pleasure in seeing him blush. "Why don't you go get changed so we can get to headquarters to get your school transfer papers filled out? And maybe get you fitted for a plugsuit."

"A plug…suit?"

"Uh right I forgot you are new to all of this. A plugsuit helps you synchronize with the Eva it's kind of like a diving suit," Misato explained.

Shinji's smile faltered slightly at the mention of the Eva, but he made an effort to not look completely distraught. "Oh, that sounds like it would be uncomfortable," he said trying to hide his disappointment. "I guess I will uh, go get dressed." He began to walk back to his room not noticing the frown that was on Misato's face.

As she watched her young charge walk away she couldn't help but feel sorry for him. She thought back to the moment when Shinji was told he had to pilot a giant mechanical monster to save mankind. It was unfair to put that type of burden on someone especially someone like Shinji. Misato let out a small sigh and then began to make her way to her bedroom to change into something more work appropriate; her mind weighing heavily on that of her young charge.

* * *

Shinji stared out of the passenger side window watching people and buildings flash by as Misato drove towards Nerv headquarters. He was not looking forward to going back to the place where his father worked. He wanted to hate his father; he wanted to give up on trying to get approval from the man who abandoned him. In the end he was the only living family he had left, and if his father didn't want him, who would? Shinji's thoughts were interrupted by a slight jolt from the car. Not realizing that he had zoned out so badly he failed to notice that they had finally arrived at one of the many car transports that led down to the geo-front. As the transport broke into the open air of the geo-front he couldn't help but feel impressed by the view before him.

"It really is beautiful don't you think?" Misato asked almost as if she was reading his mind.

"It is one of the most amazing things I have ever seen," Shinji admitted, a hint of awe in his voice.

Misato gave a slight noncommittal hum as a response. Looking out of the driver's side window, she looked down at the bottom of the geo-front taking in the sight of Nerv headquarters. The giant pyramid jutted out from wilderness that surrounded it making it seem out of place. Connected to the structure was an inverted copy of itself creating a giant manmade lake that seemed to serve no purpose other than a lame attempt at modern architecture. Her view of the building was suddenly interrupted as the transport made its way into a tunnel that signaled that they were almost to their destination.

Misato stole a glance of Shinji as he continued to stare out the window regardless of the lack of view. She couldn't believe this was the same boy that showed so much ferocity when he piloted the Eva for the first time. There had to be something more to him. Even without previous training he achieved a sync ratio that took the first and second child years to reach. Then to top it all off he hid in that shell of his acting timid and weak.

'_On the plus side though he is a really good cook_,' she thought to herself.

Looking at the young man she couldn't help be see a younger version of herself sitting there. After witnessing second impact first hand, she had spent many years secluded away from others. It had taken years of therapy for her to break out of her self imposed emotional prison. From the little information she gained through his psych profile she could understand some of his frustration. Getting thrown into a life or death situation by a father he hated yet still wanted acceptance from, she knew exactly how he felt. As the transport came to a rest at the bottom of the elevator Misato nodded to herself, she would do everything she could to help Shinji break out of the prison he had created for himself.

A/N: Well here is the first chapter, I don't know how long I plan to make this fan fiction, but I already have a lot of ideas thought up. Hopefully this is better than my previous works; it has been years since I have even tried writing anything. Thanks for reading and please review.


	2. Chapter 2

A/N: I would like to thank everyone who left me some great reviews I really appreciate. I really like how this fic is turning out compared to some of the stuff I have written in the past. I don't know how long exactly this fanfiction is going to be but I do have a lot of ideas that I want to use. Again thank you to Mazoku-sempai for beta-ing the chapter for me. Well here is chapter two read and enjoy!

The Barriers that divide our hearts: Chapter Two

Shinji grimaced as he did his best to not pick at the material that clung to his skin. How this suit was supposed to help him improve his synchronization with the Eva was beyond him, but to say it was uncomfortable was an understatement. Turing around he looked into the mirror that was in the changing room, studying himself in the plug suit that he had been issued. He took a moment to admire himself, admitting that he at least looked cool wearing the skin tight garment. The top was a pristine white color with slight shoulder pads. The lower half was mainly a dark blue with streaks of black that ran down the outside of his thighs.

Shinji's thoughts where interrupted by a small cough that came from behind him. About facing quickly, he was greeted with the sight of Misato standing there with her arms crossed, a small smile on her face. Seeing her standing there he was overcome with a sudden desire to cover himself. Looking around the changing room quickly he could not find anything within arm's reach so he crossed his arms in front of him doing his best to cover as much of his front that he could.

"Shinji calm down you aren't naked. And even if you were you don't have anything I haven't already seen," Misato laughed as Shinji blushed a deep crimson.

"Mi-Misato what are you doing in here? You said you were going to wait outside!" Shinji said as he did his best to bring his arms back down to his sides.

"Well I was, but you were taking so long I decided to come in here and make sure you were okay," Misato responded, her devious smirk never leaving her lips.

Shinji attempted to glare at her as best as he could. "I'm not a five year old Misato. I think I can manage to change my own clothes."

"Oh come on Shinji-kun I'm just teasing you. You don't have to get so upset about it."

"I-I'm sorry Misato I didn't mean to snap at you. It's just that this suit is really uncomfortable."

Misato moved forward and placed her hands on Shinji's shoulders and gave him a small smile. She was trying her best to reassure the young pilot, but she realized she had no idea how to do that. As she stood there with her hands on his shoulders, she could feel him stiffen under her touch. Seeing the discomfort in his face she removed her hands and stepped back way from the teen.

"We should head down to the Eva cages. Ritsuko said she wanted to run a few sync tests with you wearing the plug suit."

Shinji frowned at the mention of Eva, but after a brief moment he nodded and started towards the door. Misato stood aside and let him pass, her eyes slid down his backside as he walked toward the door. After a brief moment she looked away quickly as she slapped herself mentally. '_Where the hell do you think you are looking woman? He is half your age and just a kid at that_.' As she was mentally berating herself Shinji stopped in the doorway and looked back at Misato.

"Is there something wrong Misato-san?"

"Uhh...no. Everything is fine we should hurry up and get to the cages before Ritsuko gets mad."

Shinji stared at her for a second longer before turning around and making his way out of the locker room.

* * *

As Shinji sat and thought to himself he decided he hated being inside the entry plug of Unit-01. The second time syncing with the Eva was no easier than the first time. Even though he knew that he would not drown in the amber liquid, it did little to ease his fear as it entered his lungs. His anxiety was quickly replaced with boredom once the test started. Ritsuko was very unhelpful with her instructions on synchronizing with the Evangelion. With little else to do he closed his eyes and tried his best to concentrate.

"Shinji we need you to focus. Your sync rate is fluctuating too much." Shinji's eyes snapped open as he heard the blond doctor's voice over the com system.

The teen sighed softly to himself as he adjusted in his seat trying to find a more comfortable position. '_I guess closing my eyes is out of the question_,' he thought to himself. As he did his best to concentrate he noticed that Ritsuko left the video feed open letting him see what was going on in the control booth.

Shinji snorted slightly at the scene that was on the video screen. In the background he could see Misato sitting on a chair slowly spinning in a circle. As the chair spun she kept he gaze fixed on the ceiling as if it was the most interesting thing in the world. '_I guess she is just as bored as I am_.'

His thoughts began to turn to that of his purple haired guardian. He knew that he was a horrible judge of character, but Misato seemed friendly enough.

'_Maybe a little too friendly_,' whispered a small voice in the back of his head. He frowned at that thought. '_Why would someone like her bring a complete stranger into her home unless she wanted something from you_,' the voice whispered again.

He thought back to the time he spent living with his teacher. The man only kept Shinji around for the monthly checks his father sent, and to have someone cook and clean for him. There was never any conversation or anything remotely like a relationship. His teacher acted like Shinji was a burden he was forced to carry and resented him for it.

'_Maybe this time will be different. Maybe she really does want me around at least to keep me out of the Nerv barracks_,' he thought to himself.

Pushing the thoughts out of his mind, he closed the video link and once again tried to focus. Sighing once more, he closed his eyes again without meaning to. He moved his thoughts to the purple behemoth that he was trapped inside of.

* * *

Misato could not be any more bored even if she was locked in a white room with nothing but a paperclip to play with. As she spun in her chair she noticed out of the corner of her eye the video link to Unit-01's entry plug close. After staring at the console for a few moments she shrugged her shoulders.

'_Maybe he just doesn't want any distractions,_' she thought to herself. "So what's the verdict doc?" Misato said as she spun her chair to face the blond doctor.

Ritsuko frowned at her longtime friend's question. "He seems to have a hard time concentrating, but his synchronization ratio has peaked at 55.00675% when he was focusing."

"55% are you sure? Didn't it take the first and second child years to even get close to that number?" Misato asked in a disbelieving tone.

"Of course I'm sure I just don't have any way to explain it," Ritsuko replied irritably.

"Geez Rits chill out. Maybe the kid is just a natural. He did pilot the Eva the first time without any training so it couldn't have been a fluke. "

Ritsuko removed her glasses and sat them on the console and sighed heavily. She leaned back against the console and began to slowly massage her temples with her eyes tightly shut. After what felt like an eternity to Misato, the bottle blond doctor finally opened her eyes to stare at Misato with a weary look.

"I suppose that is possible. There is still a great deal that we do not know about how the Evas function. With only two other pilots to draw data from it could be that Shinji is just a better candidate for the Evangelion."

"It's kind of tragic that Shinji is doing so well, yet he wants nothing to do with the Eva unlike the others," Misato responded with her eyes downcast.

"That's pretty sentimental even for you Misato, already getting attached to him?"

"Don't be stupid Rits, It's just that I see a lot of myself in him. Our histories aren't that different."

Ritsuko sat quietly staring at her friend, her last response throwing her off. She knew about Misato's past from what she read in her personnel file, but never actually talked with her about it. After reading through Misato's files she learned that the purple haired woman had a rough life even before second impact occurred.

She spent most of her childhood moving around all over the world, never staying in one location for more than a year. Her father Shinichi Katsuragi was a well-known scientist of his time, whose field of study was biological engineering. Because of his expertise, Shinichi and his family moved often and never stayed in one place for long. Her father had a great passion for his work and his research pushed the boundaries of his field. While Shinichi was a brilliant scientist, he was a terrible father, and an even worse husband.

Ritsuko never found out the name of Misato's mother. For whatever reason, her name was never recorded, but she felt sorrow for the woman none the less. From what she could gather it seemed that Misato's mother suffered from intense depression and had suicidal tendencies. With her father always at work and her mother always locked in her room, Misato was always alone.

Between constantly moving and having emotionally distant parents the young girl never had any friends. According to the psych reports Misato spent most of her time locked in her room listening to music in attempt to drown out the sound of her mother crying. Misato blamed her father for everything, believing the only reason he drug her and her mother all over the globe was out of some twisted sense of guilt.

On July 20th 2000, two months before second impact, Misato's mother died from an overdose of sleeping pills. The tragedy struck the young girl hard. She refused to even leave her room following the week of her mother's death. After Shinichi learned of his wife's passing, he buried himself in his work not even stopping to arrange for her funeral; leaving his daughter to fend for herself.

Almost three weeks later Shinichi was chosen to lead an expedition to Antarctica to investigate irregular thermal temperatures that began to form in a centralized location. With very little option, Shinichi brought his daughter along with him to the frozen wastes of Antarctica. From what Ritsuko read of Misato's interviews, her father tried numerous times to make amends with her, but with years of pent up anger and resentment she spurned Shinichi at every turn.

On September 13th, 2000, the Katsuragi expedition made contact with the first angel known as Adam. That was the day the world almost came to an end. Misato was the only known survivor from the expedition force, she was found several days later in an escape pod barely alive. It was later revealed in one of her therapy sessions that her father was the one that brought her to the safety of the escape pod. It would haunt her for years to come that a man that seemed to want nothing to do with her gave up his life to save her.

Following the events of second impact Misato was moved from one government compound to another undergoing numerous interviews and psych evaluations. Governments from all over the world wanted to know the truth of what happened in Antarctica. On the few rare occasions that the therapists managed to get the young girl to talk they received very few details. The only thing she remembered was "a giant made of light" and then her father's face as he placed her in the escape pod. The U.N. later released a statement saying that an object only tens of millimeters in diameter crashed into Antarctica traveling ten percent of the speed of light, causing the catastrophic disaster and knocking the earth off of its axis.

It would take years of therapy before Misato would be able to function on her own. After being deemed physically and mentally capable, and signing numerous non-disclosure agreements, Misato was released from government care. She would eventually go on to attend a military run college where she excelled in advanced tactics and planning. After graduating she served two terms of service in JSDF where she quickly climbed the ranks and obtained the rank of captain. Then within the last year she was recruited into Nerv as the tactical operations director.

Ritsuko could understand how the purple haired captain would be drawing parallels between herself and her young charge. The thought was slightly disturbing though. Would this affect her judgment during an engagement with an angel? Would she be able to make the necessary decisions when the time came? She would have to bring this up at her next briefing with the commander.

"Rits are you okay? You are kind of spacing out." Misato asked as she waved her hand in Ritsuko's face.

"Yeah, I was just thinking of what other tests we will eventually have to run on Shinji," the blond replied slowly.

Misato threw her hands up in the air in exasperation at her reply. "C'mon Rits give the kid a break, this is only his second time in that behemoth and you have had him pickling in there for over 3 hours now. I think he deserves a break."

The doctor began to rub her temples with her eyes closed tight. "Fine we will postpone the tests to a later date, if only to just get you out of my hair."

Misato clapped her hands together and bowed deeply before replying excitedly. "Thank you Akagi-san, I am deeply grateful for the kindness you have bestowed upon my young charge."

Before she could reply Misato jumped up and made her way to the nearest console and opened the vid-link to Unit-01's entry plug.

"Good news Shinji-kun, the mad scientist is letting you go early today, so just give us one second and we'll get you out of there so you can go get washed off."

Shinji looked slightly surprised by Misato's appearance, but managed to express his gratitude over getting out of the sync test early.

"Don't worry about it Shinji, just head down to the locker rooms and get a shower. I will brief you on your performance when you are done." Misato replied. The young pilot nodded quickly before his vid-link cut out.

* * *

"Why am I even here?" Shinji thought to himself as yet another message popped up on his school provided laptop. He had been messaged constantly since class started, all of them asking the same thing. "Are you the pilot of that giant robot?" He resisted the urge to glace around the class room he knew that everyone was already looking at him eagerly waiting for his response. He closed his eyes as he sat his hands on the keyboard. He was getting ready to type out a response when he remembered the conversation he had with Misato that morning.

It had been an eventful morning for Shinji as he was still getting used to Misato's unusual morning behavior. How drinking beer in the morning could wake anyone up was beyond him. After finishing breakfast he went back to his room to get ready for his first day of school in Tokyo-3. Giving himself a once over in the mirror to make sure there was no reason for anyone to make fun of him. Grabbing his bag and the new cell phone Misato had given him he left his room and made for the front door. As he was putting on his shoes he heard a small cough from behind him.

"Shinji before you go there is something I want to talk to you about," Misato said as she nervously shifted from one foot to another.

"Y-y-yes Misato-san," Shinji managed to stutter out. '_Please, please don't tell me I can't stay here anymore_,' his mind screamed as he tried his best to make eye contact with his purple haired guardian.

"It's nothing that serious, it's just about school…and piloting," she replied with a slight pause. Before he could reply Misato stepped forward and put her hands on her young charge's shoulders. "There is no rule or anything that says that you can't tell anyone that you are an Eva pilot, but for your first day of school I think you should really keep your head down and not draw too much attention to yourself."

Shinji's head snapped up with a look of surprise on his face.

"I just don't want you to make things harder for yourself then they need to be. Starting a new school is going to be tough enough." Misato stepped away to give Shinji and folded her arms across her chest. "Some of the students are going to put two and two together, so a new student showing up right after the fight with the last angel is going to be very suspicious. Don't be surprised if they ask you if you are the new pilot."

"Why would they think I'm the pilot, wouldn't I be considered a little young to be piloting a robot the size of a skyscraper?" Shinji asked with a little edge in his voice.

Misato laughed at his sudden outburst. '_So he can be assertive_,' she thought to herself. "You will be in the same class as Rei Ayanami, so they most likely know that the Evas are piloted by teenagers."

Shinji froze at the mention of Rei's name. He had yet to see the blue haired pilot since their first encounter in the Eva cages, but he was told that she was recovering just fine.

"So what should I do if they ask me?" Shinji asked slowly.

Misato smiled slightly at his hesitation. "I can't tell you what to do Shinji-kun, you are going to have to figure that out for yourself. If you want to tell them that you are the pilot you can, but like I said I don't want you to make things harder on yourself."

Shinji looked confused by Misato's answer, but didn't want to say so. He did managed to struggle out an, "Oh, okay."

Misato gave him her trade mark smile, "Don't worry about it too much and try and have a good day. I will see you later tonight for dinner."

Shinji blushed at her last comment but turned around quickly hoping she didn't see it, but she did. After one train ride and a short walk he made his way to school where he found himself in his current predicament. Opening his eyes to look at the screen he typed out his response to one of the many messages. "No I am not." Short and to the point Shinji thought and with that he hit the enter key.

Almost instantly the class groaned in unison. He had never felt so bad about lying, but he really did not want to disappoint Misato. Sighing to himself he shut his laptop to ignore the sting of messages that continued to pop up. Looking around the class room he locked eyes with one of the other students. He was wearing a track suit instead of the normal school uniform and Shinji could see the anger burning in his eyes. Before he could look away Shinji saw the angry jock mouth the words, "You're dead." Shinji decided that today was definitely not going to be a good day.


	3. Chapter 3

The Barriers That Divide Our Hearts: Chapter 3

* * *

It had been three weeks since Shinji had first started school and after the first day everything seemed to fall into a nice, easy rhythm. He had even managed to avoid the angry looking jock that seemed to have a grudge against him. This had come at a price though. He had already skipped cleaning duty twice now and the class rep was furious about it. After her first lecture when he skipped the second time, he quickly decided that was one woman he did not want to upset.

So once again Shinji found himself sitting in class attempting to listen to the teacher drone on about second impact. The first two days he found it slightly interesting, but after the first week it had grown old very quickly. One would think that you could only tell the same story a certain amount of times before even the storyteller got bored of hearing it. As the teacher continued to talk, Shinji's thoughts began to wander.

The last few weeks had been hectic for him, but at the same time he kind of enjoyed it. Misato's apartment was a challenge that was for sure. He spent the first three days alone just digging trash out of the place, and after clearing Misato's room out twice in the same day he eventually just gave it up as a lost cause. How that woman could generate that much trash in a short amount of time was beyond him. The dishes were a whole other nightmare all together; he ended up having to throw almost half of them out because they were so disgusting.

He made dinner every night for Misato and himself even though she was supposed to cook three nights out of the week. After the first meal he had that was made by Misato's hand he spent the rest of the night in the bathroom throwing it up. From that day on he took over all of the cooking even going so far as to make bento for Misato so she had something to take to eat at work. Her continuous compliments about it still made him blush slightly.

His thoughts were interrupted by the school bell signaling the end of the day. He rose and bowed to the teacher at the class rep's command. He quickly gathered up his school supplies and made a b-line for the door. Walking swiftly down the hall and bumping into a few students in the process, he finally made it to his locker where he pulled out his shoes. As he finished pulling on his shoes he felt a strong grip on his shoulder.

"Did you really think you could run away forever? Or did you just think I would forget about you?" the stranger questioned.

Shinji was pulled up roughly by his collar and spun around. He came face to face with the jock who threatened him on the first day of class. He began to panic. He really did think that the jock had forgotten about him.

"I-I-I don't even know who you are," Shinji managed to stutter out.

The jock smirked, "The name is Touji Suzahara, and I'm here to give you a proper school greeting."

"Th-that isn't really necessary, I have been here for a few weeks now and ev-everyone seems friendly enough," Shinji said while attempting to find his voice.

"Before we continue let's find a quieter place to finish this conversation," Touji said with a devilish grin on his face.

Touji lifted him up by his collar and shoved him towards one of the hallways. They continued to walk down the hall making their way to the back of the school. Shinji could feel Touji's hand firmly clamped on his shoulder. He kept glancing out of the corner of his eye to see Touji wearing a carefree grin as he waved to fellow classmates. It was at this time that Shinji was absolutely terrified.

Before his brain could even begin to think about what the jock had in store for him they reached an alley way that separated two of the school buildings. As Shinji looked up he noticed that there was nerdy looking boy there messing with a digital camcorder. '_Oh thank god maybe he will let me go since there is someone here_,' he thought to himself.

"Yo Kensuke you ready to do this?" Touji shouted.

Shinji's face fell as he heard Touji call out to the other boy.

"Are you sure about this Touji? We really don't know if it's him for sure or not…" Kensuke said with a frown.

"Do you really believe that he just happened to move here the day after that monster tore up the city? Even if he isn't the pilot I need to take out my frustration on something, and him being the new guy and all makes him the perfect punching bag."

Kensuke looked at Shinji for the first time and bowed slightly giving him a weak smile. "I'm really sorry about how Touji is acting. You see his sister was injured when that giant robot and monster fought here in the city." He paused while he stood back up and pointed to Touji, "You see Touji here believes that you are the pilot of that giant robot that went crashing through the city."

"Enough of this bullshit I'm tired of waiting!" Touji yelled.

Before his brain could even register what was happening, he felt himself being turned around roughly. Shinji caught a glimpse of intense hatred in Touji's eyes before he felt an immense pain in his jaw. He stumbled backwards from the force of the blow and hit his back on the building behind him.

Shinji slowly slid down the wall holding his wounded jaw with his hand. He could feel tears beginning to well up in his eyes, but he refused to cry in front of these two. As he hit the ground he was overcome with a sudden rush of anger. '_I was only trying to protect them! I didn't even want to pilot that damn thing and this is what I get_?' Shinji thought bitterly. He slowly started to get back up with his head hung low.

"Do you think I wanted this? Do you think I wanted to get into that… beast!?" Shinji spat.

"I didn't ask for any of this!"

Shinji was thrown back once again as Touji punched him in the jaw once more. He hit the ground hard and had the wind knocked out of him. He could see the form of the two boys towering over him as he lay on the ground.

"I really don't care what you want. It doesn't change the fact that your hurt my sister because you didn't know what you were doing," Touji growled.

"C'mon Kensuke let's get out of here."

Shinji could feel the footsteps as Touji walked away, but he could still see the shadow of Kensuke looming over him. He closed his eyes to block out the bright sun and hoped that the other boy would just go away.

"I'm sorry for how he acted; he is really a nice guy once you get to know him. I think he is angrier with himself that he couldn't help his sister than he is with you." Shinji didn't say anything to that choosing to remain still instead of replying. After a few moments he heard Kensuke sigh. "I'll make sure Touji doesn't say anything about you being the pilot, you must have your reasons for not wanting others to know."

For the one millionth time as he lay on the hard ground he wondered why he piloted the Eva, and why he continued to try.

* * *

"I'm home," Shinji called as he kicked off his shoes. He was home about an hour later then he usually would be, but he hoped Misato wouldn't notice.

"What took you so long Shinji-kun? You were out a bit later than usual. Finally get yourself a girlfriend?" Misato teased from the kitchen.

Shinji sighed. He was hoping to avoid his guardian, she was sure to ask questions about the bruises on his face. He made his way toward the kitchen and peaked around the corner, '_Maybe I can sneak past her and get to my room._' Shinji thought to himself. As he peered into the kitchen his vision was suddenly filled by the ample bosom of his purple haired roommate.

"See something you like?" she said in a light tone.

Shinji's face flushed red and he turned his head quickly to keep himself from staring. This, much to his dismay, gave Misato a clear view of the bruise on his jaw.

"Shinji-kun what happened to your face? Did you get into a fight? Who did this to you?" she asked quickly while she gently grabbed his head so she could better inspect the damage.

"It's nothing Misato. I'm fine I swear." Shinji replied while avoiding looking into her eyes.

"This is not 'nothing' Shinji. Either you tell me what happened or I get section 2 to tell me what happened." There was a pregnant pause between the two before the captain spoke again. "I would rather hear it from you."

Shinji finally looked up and locked eyes with Misato and he saw something there that he had never seen before. She cared, not just about him as her charge but as a person. In her eyes was a compassion he had never seen from another. Shinji could almost feel the warmth radiating from her as she continued to hold his face, and was left speechless as he continued to stare into her eyes. He never noticed how pretty they were until that moment, and knew then that he could not lie to her.

"I… yeah I kind of got into a fight," Shinji finally replied.

"How did this happen? Who did you fight with?" Misato asked insistently.

"It was fairly… one sided. It was with someone from my class. I didn't fight back I just let them hit me."

"Why Shinji? Why wouldn't you fight back when someone was attacking you?" She replied quickly.

"His s-sister was hurt in the angel attack; he found out that I was the p-pilot. I felt horrible and didn't know what to do so I just let him hit me."

All of the pain and worry that he felt earlier in the day came rushing back, he could feel tears beginning to well up in his eyes. '_Please not now, not in front of Misato, I don't want her to see how weak I am._' Shinji thought to himself. He closed his eyes and willed the tears to go away anything to keep his guardian from thinking less of him. His eyes snapped open as he felt himself being embraced; his vision was obscured by locks of violet hair.

"Shinji I understand what it's like to be afraid and alone, but you don't have to be alone anymore. I will be here for you so you don't have to go through the same thing that I did." Misato said as she continued to hold Shinji.

Shinji was shocked by her words, '_Why would anyone care about me? No one has cared before; so why her?_' Shinji thought to himself. As he stood there with her arms around him he decided that he didn't care what reason she had or if she was lying to him, right now he was alone. He slowly brought his arms up and wrapped them around her back as she held him tighter.

"I… I'm sorry that I am so weak Misato." Shinji mumbled into her hair.

Misato rubbed his back gently for a few moments before responding. "Shinji you aren't weak, you have been forced into a situation that no one should have to deal with. I actually think you are handling everything pretty well. Most people in your position would have run at the first chance they got."

"Do you really mean that?" Shinji asked as he pulled away from her.

"Yes I do Shinji, what you did in the Eva was a great thing, you saved this city and everyone in it."

"Th-thank you Misato I really appreciate it. I'm really glad I met someone as kind as you." Both Shinji and Misato blushed at his last comment.

"Well I don't know about that, but if you want there is something I think I can do to help you out."

Shinji blushed even deeper at Misato's response while his mind went to a very dirty place. "I-I-I-I don't th-think that is necessary Misato-san." Shinji stuttered.

Misato laughed as she realized how that must have sounded. She was also not one to pass up on a chance to tease her young charge. "Ohhhh Shinji, I didn't know you were interested in me in that sort of way. I always was into younger men though." Misato said in a sultry voice.

"Mi-misato-san!" Shinji yelped.

"Shinji-kun you are so easy to tease," Misato said with a soft smile on her face.

With their problems momentarily forgotten they both basked in the warmth of the other. After several minutes of silence Shinji began to feel uncomfortable in Misato's embrace. It wasn't that he didn't enjoy being held by Misato it was just that he was starting to feel embarrassed from such a hold after so long.

"So what did you think you could do to help me?" Shinji said as he broke away from Misato's embrace.

"It's an idea I have been toying around with for the last week, I really think it will help you both in and out of Eva." She replied with a wolfish smile on her face.

"Wh-what could that be?" Shinji said suddenly worried.

"Easy Shinji-kun, I'm going to put you through weapons and combat training."

* * *

Deep within Nerv headquarters, there was a giant room that most of the staff went out of their way to avoid. Most said that it was cursed and that anyone who entered the room never left and that their souls were trapped there forever. In reality the room was the office of Gendo Ikari commander of Nerv. One would think that his office was designed to be intentionally intimidating. It was a bare room completely bare except for a giant desk that dominated the center of the room. The floor and ceiling were decorated with some sort of intricate pattern. The only light in the room came from Gendo's desk itself; it would reflect off of his glasses and completed his menacing image.

On that day, like any other, Gendo sat at his desk with his hands folded into a bridge that obscured his face, and his second in command Kozo Fuyutsuki stood next to him. Fuyutsuki glanced at Gendo out of the corner of his eye as he wondered how someone could sit in one position for so long. Several long minutes passed before either of them moved. It was a subtle gesture on Gendo's part; just a slight straightening of the back, but it was enough to let Fuyutsuki know that he was allowed to talk.

"Ikari are you sure we should allow the Third child and the captain to get so close this early in the scenario?" Fuyutsuki asked.

"It makes no difference how close they are at this moment. It will only further serve our purpose when the time comes." Gendo replied without even glancing at his old professor.

"Don't you think the Third will be less pliable if he has something to fight for?"

"Having something to fight for is what will allow us to control him. With a push in the right direction we will be able to have him comply with whatever we need."

'_How can one man be so cold to his child?_' Fuyutsuki wondered for the hundredth time. He knew what they were doing was going to go against the vision that Seele wanted to complete, but he knew it was necessary if he wanted to see Yui again. He was startled out of his thoughts by Gendo's head shifting slightly.

"Inform Dr. Akagi that she needs to make the dual plug insertion system a priority. We need to be able to implement the system as soon as possible."

Fuyutsuki nodded his head knowing that Gendo saw the motion even if it seemed like he was not looking. He turned and began to walk away from the desk but stopped at the corner with his hand resting on its surface.

"Are you still sure about this Ikari? Soon we will reach the point where there will be no turning back," the old professor said without looking at Gendo.

"Kozo… you and I both know that we passed the point of no return a long time ago. We have no choice now but to move forward," Gendo replied coldly.

Fuyutsuki nodded slightly and then continued forward towards the door. '_I hope you will forgive us Yui for what we are doing_.' He thought to himself. '_Only time will tell_.'

* * *

A/N: Well here is another one, it's a bit shorter then the other two. Let me know what you guys think, I'm trying to develop Misato and Shinji's relationship at a some what slow pace. I don't want it to be like they confess their undying love for each other even though they just met. Once again thanks to Mazoku-sempai for the beta.


	4. Chapter 4

A/N: Sorry for getting to this chapter so late, I was having troubles with my beta getting to this chapter. I feel as if this chapter was very heavy on interactions between Shinji and Misato, but there should be much more action in the next chapter. Thanks for reading and please leave a review letting me know what you guys think. As always thank you Mazoku-sempai for the (late) beta!

The Barriers That Divide our Hearts: Chapter 4

_I don't think I am going to be able to move for the next week,_ Shinji mentally groaned to himself as he lay in his room. He had just taken a hot shower to help soothe his aching muscles and his damp hair was starting to get his pillow wet. When he felt the water start to spread down his back, he did his best to roll over to grab the towel he had discarded when he first entered his room. _God, how does she expect me to do this every other day?_ he wondered as he let out a small groan, his body protesting against the unwanted movement.

Shinji thought back to the intense workout that Misato had put him through. Before they even had even started Shinji thought he was going to pass out the moment he saw Misato walk out of the womens locker room. Since this was supposed to be part of his training as a pilot he figured his guardian would dress a little more conservatively for their workout. It seemed that the purple haired vixen did not want to pass up any chance she had to make her young charge flustered.

The first thing he noticed was the tight purple tank top she was wearing that covered the black sports bra underneath. His eyes slowly slid down, the tank top stopped just above her navel leaving her midriff exposed and revealed her creamy white skin. As his eyes continued their downward journey, he noticed the way her black workout shorts hugged her hips nicely. His thoughts were interrupted by a loud cough from Misato. His eyes snapped up to see a giant grin plastered on her face.

"Now I know you see something you like," Misato teased.

Shinji's face turned a bright red as he fumbled over his words trying to form a coherent response. Misato couldn't help but laugh at her charge's obvious discomfort.

"Shinji-kun it's perfectly okay for you to find a woman as beautiful as myself attractive. I think I would be more offended if you didn't ogle at least a little bit."

"Misato-san!" he shouted, as he looked away, face still flushed.

Misato clapped her hands together to get Shinji's attention. When he turned his head to face her again she did her best to give him a soothing smile. "Alright Shinji we are going to do some stretching first before we start so you don't hurt yourself."

Shinji gave her a nod and a weak smile in response. Misato began to walk him through various different stretches and he was baffled by how limber she was. After several minutes, his guardian told him that it was time to get started on the actual workout. Thus began the most excruciating two hours of his life.

When they finished Shinji was covered in sweat and his muscles screamed in protest every time he moved. Misato on the other hand hardly looked winded at all. As he lay on the gym floor he let out a small groan as she looked down at him; her trademark smile still plastered on her face.

"Oh is my little Shinji-kun worn out already?" she teased.

"How are you... not tired?" Shinji questioned between large gulps of air.

"I work out three times a week. How else do you think I keep such a nice figure?" Misato asked as she leaned forward to help him up.

When she did this Shinji was greeted with a nice view of Misato's cleavage. He did his best to look away as he reached his hand up to grab hers, but the first thing his hand touched was definitely not her hand. His eyes quickly looked to his hand and was terrified to discover it pressed firmly against the purple haired beauty's bust. The first thought that popped in his head was, _Oh my god, I'm going to die!_ but when his gaze finally shifted to Misato's face, he was once again greeted by her devilish smile.

"My my Shinji-kun, you are getting more bold every day," she said with a glint in her eye.

Shinji, to his credit, did not pass out on the spot, but he quickly withdrew his hand and began to stutter out an apology. As he continued to panic Misato reached down to grab his hand and then pulled him up to his feet. When he was back on his feet, he avoided looking at Misato; too embarrassed to face her.

"Shinji calm down it was an accident. You don't need to get so bent out of shape," Misato said trying to console her young charge.

Shinji took in a large breath as he tried to calm himself. "I-I know Misato-san, I just don't want you to be mad at me," he managed to say dejectedly.

She was taken aback by his response. _Mad? Why would I ever be mad at him?_ she thought to herself. Putting one of her hands on his shoulder, she used her other to tilt his head up. As she looked into his eyes she could see his burning need for acceptance.

"I know you better than that Shinji-kun. I know you aren't the type of person to cop a feel when given the chance. Plus it's not like I'm complaining. It has been awhile since I have gotten any action myself," she added teasingly.

Shinji's face lit up like a lightbulb at her response as his mind was flooded with images of his guardian with far less clothing than she had on now. He did his best to banish such thoughts from his mind. It wasn't right for him to think such things of someone who was being so kind to him. Shoving his worries to the side and laughing slightly he stepped away from his guardian. He decided maybe it was time to give her a taste of her own medicine.

"With someone as pretty as you Misato-san, I highly doubt that," he deadpanned.

At first Misato thought she had misheard her young ward, surely he wouldn't have said something like that. Then it hit her like a sack of bricks, he was teasing her. With a huge smile on her face she grabbed the teen in a headlock and began to to vigorously rub his scalp with her fist.

"I'm so proud of you Shinji-kun, that is the first time I have heard you make a joke. And at my expense no less!"

The young teen flailed about as he tried to escape from the woman's iron grip, but he found himself laughing along with her. _Maybe I finally found a place where I belong,_ he thought to himself as the purple haired beauty finally let him go. He attempted to stand up straight, but was quickly reminded of the intense two hour workout that he had just gone through. She had only felt slightly bad about putting him through such a rough workout for his first time, but it was for his own good.

"C'mon Shinji-kun! Since you did such a good job today I will help you hobble to the locker rooms. And if you're lucky I'll even help change your clothes," Misato said with a wink.

His cheeks flushed once again, but he was much too exhausted to form a response. Instead he nodded dumbly. Misato pouted slightly at his reaction. _It looks like I may have pushed him a little too hard,_ she thought to herself. She decided that the best course of action for right now was to get him changed so he could get home and get a hot shower.

* * *

Finally managing to roll over and get out of bed Shinji, decided he should go and get started on dinner. Walking stiffly, he made his way to the kitchen where he found his guardian in her usual evening attire of a yellow tank top and cut off denim shorts. She gave him a small smile when he walked in and tipped her can towards him in greeting.

"How are you feeling?"

"Not as bad as earlier, but I'm still pretty stiff," he said as he stretched to emphasize his point.

"That's good to hear, but don't worry about it too much. Once you start working out regularly it doesn't hurt nearly as much afterwards." she replied

Her young ward nodded in understanding and set to work on cooking dinner for the both of them. Misato sat quietly and nursed her beer as she watched Shinji quickly move about the small kitchen. One of the things she found amazing in the teen was his ability to cook. She had been pleasantly surprised the first night he cooked by how good the meal tasted, and afterwards gave no complaint on his insistence to cook dinner every night.

As if sensing her thoughts, her stomach let out a loud growl, slightly surprising the woman. She covered her mouth and laughed to try and hide her embarrassment as Shinji turned to look at her.

"I guess I'm a lot more hungry than I thought," she said while waving him off.

"Well the food should be ready in just a few minutes, so you won't have long too wait."

She nodded her head in response as he returned his focus on the meal. She had no idea why she even felt embarrassed to begin with. _I know his food is good, but c'mon this wouldn't be the first time you were eager for something_, she thought to herself. Brushing the small incident off, she sat quietly finishing her beer while she watched the young teen cook.

As they ate, they talked about small things like how work was going for Misato and how Shinji was doing in school. After a few minutes, they lapsed into a comfortable silence while picking at the remains of their food.

"So are you ready for tomorrow?" Misato asked while looking up from her food.

"Ready for what?"

"You really must be out of it! Tomorrow we start your weapons and tactics training," Misato replied excitedly.

"But I uhhh have school tomorrow don't I?" he said lamely trying to figure out a way to get out of more of Misato's training.

"I already let the school know that you aren't going to be attending tomorrow, so everything is covered," Misato beamed while enjoying her ward's obvious discomfort.

The young teen squirmed under the older woman's intense gaze before managing to reply. "I guess there is no way I'm getting out of this is there?"

"I promise I will go easy on you tomorrow Shinji-kun. Most of it will be discussion, so don't worry too much about it," she said with a little less enthusiasm.

"Now why don't head to bed? You deserve a good night's rest. And don't worry about the dishes I will take care of them."

He hesitated slightly knowing that Misato volunteering for chores could only lead to disaster. After a moment he finally pushed his chair back and stood up.

"I guess if you are okay with it, it was my turn to do them tonight though," he said weakly.

"Shinji-kun you worry too much. Just think of it as payment for all of the delicious food that you have been making for me," she replied warmly.

The young brunet's face flushed a bright red at her comment. He knew that he was a good cook. He had been practicing for years, but no one had ever told him that it was delicious. His uncle just expected him to cook and he never gave a word of thanks in return. Something about the way the beautiful woman in front of him so candidly complimented him made him feel warm and content deep inside. It was something he had only felt a few precious times since his mother died, but with Misato it was something different... Something new.

"I...Thank you Misato-san that means a lot to me." And with that he turned and made his way to his room.

Misato sat and stared at the empty hallway that her young ward had just walked down, a small frown on her face. _What was that all about?_ she thought to herself. _I can't be the first person who has ever said that his food was good can I?_

After a moment she gathered up the dishes, deposited them in the sink, and began to rinse them off one by one. When she was finished she dried her hands off and made her way to her bedroom. Laying down on her side on the slightly worn futon, she pulled the blanket up to cover herself. As she slowly drifted off to sleep her mind weighed heavy with thoughts of the boy in the next room over.

* * *

"I don't understand this at all Misato-san," Shinji sighed as he lowered the weapon in his hand.

"I told you for the hundredth time you are standing wrong. Here let me show you," she replied as she walked up and stood right behind the teen. Reaching out she snaked her arms around her ward one hand balancing the gun in his hand and the other grasping his elbow.

"You need to keep your arm straighter and locked or else the recoil is going to ruin your aim. You also need to relax. You are never going to be able to shoot properly if you stay so rigid."

Shinji did his best to nod. He was more thrown off by the close proximity to his purple haired guardian than trying to learn how to shoot a gun. Concentrating on the task at hand, he lined up the target once more in his sights and pulled the trigger. He was rewarded with a hit just on the outside of the mock human target getting him the closest he had been all day.

"Good job Shinji-kun! It looks like you are starting to get the hang of this. With some practice you will be sharpshooter in no time," she said while grinning from ear to ear.

Looking up at the woman, he couldn't help but notice how infectious her smile was. Grinning like a fool he flipped the safety on the pistol and turned to set it down. As he sat the gun down, he realized how much his life had changed in the last few months and the smile on his face began to slip.

"Misato-san," the boy said while still facing away from the woman.

"What is it Shinji-kun?"

"I-I... I just want to thank you for everything you have done for me, I... I don't think I would have lasted long without your help," he replied.

Frowning slightly at her ward's sudden change in mood, she paused briefly not really knowing what to say. Being more of a physical person and no stranger to skinship she did the only thing she could think of. Gathering up the young pilot in her arms, she hugged him tightly from behind. They stayed that way for several minutes before Misato finally spoke.

"No one should ever have to deal with what you are going through. If I could take your place I would do it in a heartbeat Shinji-kun. Right now the only thing I can do is be here for you and do my best to prepare you for what is to come."

Shinji let Misato continue to hold him while he basked in her warmth. He couldn't remember the last time anyone hugged him let alone tried to comfort him. Finally breaking free from her he turned around to face the beautiful woman.

"I'm really glad I met you Misato-san, I don't think I have ever known someone as amazing as you," he finished with a shy smile.

There was something about the shy boy that she just couldn't place. Sure she had been hit on by a seemingly endless amount of guys. But her ward's candid compliment struck a cord inside of her. Feeling her cheeks begin to flush with embarrassment, she smiled softly at the teen.

"I don't know about all of that Shinji-kun, but you really know how to make a woman feel good about herself."

Misato patted the now flustered pilot on the shoulder and then began to make her way to the exit. Stopping briefly she looked over her shoulder and called out to the boy. "Hurry up Shinji-kun! Since you have been doing such a good job with your training I will take you out to eat tonight, my treat."

Finally collecting himself, Shinji grabbed the weapon he had been practicing with, quickly made certain the safety was on, and then followed after his guardian. As he walked behind her he couldn't help but admire her. It wasn't just her beauty that he found amazing it was everything about her that made him like her. _I hope that one day I can be as strong as her_, he thought to himself listlessly. Making their way out of Nerv HQ, they hopped into Misato's car and headed toward the small apartment that they shared together.


	5. Chapter 5

A/N: Well here we go with another chapter, sorry it took so long to get this one out. I have a really hard time writing action scenes and I feel like I kind of copped out on this one. I also felt like I was making Shinji a bit too accepting of his current situation so I decided to switch it up a bit in this chapter. Lastly I apologize if this chapter doesn't seem as well written as my last ones. I did not have a beta for this chapter and with no editing my writing isn't that great. Well enough of that read and enjoy!

The Barriers That Divide Our Hearts: Chapter 5

Shinji's heart was pounding. It had only be two months since the last angel before the newest one arrived just off the coast of Japan. Shinji had been training diligently with Misato during that time but he still felt unprepared for the newest battle. He had spent every other day at the gym with Misato pushing his body further and further every time. When he wasn't in the gym he was at the shooting range practicing or learning new tactics from Misato. Between working out, training, and school he was thoroughly exhausted.

Once he had reached the surface of Tokyo-3 he finally saw the 4th angel for the first time. It had a long cylindrical body connected to a large head that was in the shape of a spade. It didn't look like it had any arms that he could distinguish, but he did catch a glimpse of what looked like hundreds of tiny claws on the underside of it's head. He could see it's massive red core in the crevice where it's body met it's head.

He grasped the control yokes of Unit-01 tightly in his hands as he willed the behemoth to poke it's head around the building he was hiding behind. He felt the Eva shift the rifle in it's hands bringing it up closer to it's chest. _Okay tight controlled bursts just like Misato taught me._

Bracing himself for the worst he swung Unit-01 out from around the building trying his best to line up a shot as he did so. Seeing the target reticule turn red in his H.U.D he fired two quick three round bursts and quickly moved for cover behind the adjacent building.

Peeking out once more it seemed as if the Angel hadn't taken any damage whatsoever from his attack. _I don't even know why I thought this was going to be easy. _Before he could mount another attack he saw that the Angel began to move. Long whip like appendages glowing a bright purple began to sprout from the upper portion of it's body. Shinji continued to stare at the beast until he heard shouting over the comm link yelling at him to move.

After just mere seconds of quickly diving out from behind the building it was quickly sliced to pieces by the angels flailing whip like arms. Shinji willed the Eva to move faster as the angel shredded everything in it's path as it chased him. He could hear someone yelling commands at him over the comm link, but he could not understand what they were saying. All of his attention was focused on staying one step ahead and not getting caught. After several minutes, which to Shinji felt like eternity, his luck finally ran out.

The Eva faltered after losing its footing as Shinji tried to force it around a tight corner. This mistake was all the angel needed to get a hold of the purple giant. Grabbing the Eva by it's neck it slowly hoisted it into the air with one of it's long appendages. With the other it began to snake itself around Unit-01's torso.

Shinji had to fight the urge to grasp at his throat as the neural feedback made him feel the Evangelion's pain. Focusing his mind he gave a mental command for the shoulder pylon to open, and with a push of the butterfly controls he willed the Eva to grab the progressive knife with it's free hand. With a swift motion the Eva sliced the knife through the one of the angels whip like arms, he could feel the pressure on his neck and waist relax as the angel let out a loud screech.

_I need to end this quickly before it cuts my umbilical cable_. Just as he was about to lunge at the angel's exposed core he felt the Eva's legs being pulled out from under him. To his horror the angels limb had already regenerated and was currently being used to fling the giant purple mecha across the city and into a nearby hillside. As he collided with the ground Shinji was vaguely aware of the cockpit turning red as the Eva switched to internal power leaving him with only a few minutes to either win or run out of power.

* * *

"I don't believe this, every channel is blocked it's complete censorship!" Kesuke shouted as he slammed the LED screen on his camera shut. The young teen gripped his camera tightly as he fumed. _It just isn't fair, how come I can't even get a glimpse of that giant robot._

Touji grunted in response not really paying attention to his otaku friend. He was more interested in getting a peek of underwear from the girls sitting across the shelter. _How can they shift their legs so much and not expose anything?_ His musings were cut short as Kesuke hit him in the back of the head with a rolled up magazine. "Are you even listening to me?" he seethed.

The jock finally turned to look at his friend, but not before one of the girls noticed his line of sight and gave him a dirty look. _Good thing it wasn't the prez, she would have gutted me like a fish. _While he did sort of like the class president he definitely did not want to be caught trying to look up her skirt. He mentally cringed when he thought about the last poor soul that she found had been taking pictures of the girls while in the locker rooms. _And he didn't walk right for a month after that either, _he thought to himself.

"Sorry Ken, I really wasn't paying attention," the jock finally responded while rubbing the forming sore spot on his head.

"The blackouts! That's what I'm talking about. can you believe they are doing this? As citizens we have a right to know what is going on out there." Kensuke was practically yelling by the time he finished his sentence.

"There isn't a lot we can do about it ya know, NERV pretty much runs everything around here. So if they don't want to go showing off their giant toys to everyone then they just blackout the media." Touji replied evenly.

Kensuke stood up quickly startling Touji slightly as he did so. "I need to see it, this may be the only chance I ever get." Turning around the young nerd began to make a beeline for the exit. Not knowing what to do Touji jumped up and chased after his friend while calling over his shoulder. "Hey prez we need to go to the bathroom!"

He couldn't make out what she yelled back, but he imagined it couldn't have been anything nice. He made it to the exit and saw Kensuke out of the corner of his eye. Rushing after him he caught up with him quickly as he was trying to decide which way to go. "Do you remember how to get out of here?" Kensuke asked.

Touji glanced down both hallways trying to remember which way they had come in from. After a moment he was hit with a realization of where they were. "Won't we have to go up since the buildings retract underground during emergencies?" Kensuke's eyes lit up at the jocks question, "Of course! How could I forget something like that?"

Without even waiting the otaku took off toward the nearest stairwell. Touji ran after him, and had a hard time catching up despite being in better shape than his nerdy counterpart. "I guess when he is excited about something there is no stopping him." As they climbed each flight of stairs he couldn't shake the feeling that something bad was going to happen. 'Just a quick glance then we high tail it back to the shelter.' Even he didn't believe that was going to happen.

* * *

Everything hurt. Shinji let out a low groan as he forced his eyes open grasping his head in both hands as he did so. Everything was a blur of colors and loud noises to the young pilot, making it very difficult to regain his focus. The first thing he began to notice was the yelling over the comm link. "Shinji! Are you alright? You need to get up now, the angel is headed right for you and your umbilical cable has been cut! You only have three and a half minutes of power left!" Misato yelled.

Looking up as his vision began to clear and he could see the fourth angel floating towards him. Then another alarm began to sound signaling that there was another human presence close to the Eva. Hesitant to take his eyes off of the angel he glanced to where his H.U.D was indicating the interference was coming from. He inhaled quickly when he realized who was caught between his Eva's fingers, it was the two boys from school that beat him up.

"Shinji you need to move now!" Misato yelled.

Snapping to attention he noticed the angel was much closer and would be on top of him any second. "Misato-san I can't move there are two people trapped between the Eva's fingers, if I move now they will get crushed." It was several seconds later after he heard muffled chattering over the comm when Misato spoke again. "Shinji lock the Eva into it's current command and then we will eject the entry plug so you can let them inside."

Before Shinji could respond the angel was upon him. He reacted quickly and grabbed the angel's whip like arms and cried out at the sudden pain in his hands. Giving a quick mental command the entry plug went dark as the Eva continued to hold the angel and the plug ejected. He could hear Misato's voice booming over the loudspeaker outside of the Eva telling the two young boys to get into the entry plug.

After several tense moments Shinji began to panic. _They are taking too long, I'm going to run out of power if they don't hurry._ Before his thoughts could go any further he heard a splash and one of the boys began to sputter. Not wasting any time he willed the purple behemoth back to life. "Shinji I need you to listen carefully, you have less than a minute and a half of battery power left. I want to retreat using route D and use elevator 132, we need to regroup and prepare another attack."

The young pilot barely heard Misato as he looked at the battery timer quickly racing closer to zero. 'I have 75 seconds left of power there is no way I'm going to make to the elevator' he thought to himself with fear. As he turned his gaze to the angel that he still held tightly to something inside of him snapped. _Why am I even here? Why am I doing this? I'm no one special so why am I stuck with this responsibility?_ His anger flared, _What did I do to deserve this?_

Shinji gripped the controls tightly as he brought the Eva's foot up to the angel's chest and with a single thought launched the beast away from him. Picking up the progressive knife from where it had fallen he quickly stood up to face the angel. He could feel the vibration of the humming blade and he could hear the two boys blabbering about running away. Everything but the enemy in front of him washed away as his anger continued to rise. With only 35 seconds of power remaining, and numerous people screaming at him to run away, he charged forward to meet the angel head on.

* * *

"What the hell do you think you were doing out there?" Misato asked sternly. Shinji sat on one of the locker room benches hunched over with a cup of water clasped in his hands. He gave no response to his guardian-commander and continued to stare at the floor. "You violated a direct order and instead recklessly attacked the enemy. You could have gotten yourself killed out there." Grabbing her charge by the shoulder she pushed him upright so that they were face to face. "Do you understand what I'm saying? You could have cost us everything, when you are out in the Eva you are required to follow my orders to the letter."

"We won didn't we? That's what matters in the end right?" Shinji asked as he jerked out of her grasp. "No it is not, what matters is your ability to continue to pilot the Eva." She responded

"That's what this all comes back to isn't, everyone is happy if I just shut up and pilot aren't they" Shinji hissed. "I never asked for any of this!"

Misato stepped back and crossed her arms over her chest "No one is forcing you to pilot, it always was and still is your choice to pilot." Shinji was taken back by her statement. He quickly recovered and stood up to face Misato. "What do you mean it's my choice? According to everyone here at Nerv I have to pilot or a lot of people will get hurt and die, so how do I have a choice in piloting?"

"There is always a choice Shinji, there is no one making you stay here. If you can't follow my orders when you are out there then you are more of a danger to others than if you weren't piloting at all."

Shinji's face hardened at her response. "Fine then if it's my choice then I want nothing to do with Eva or Nerv ever again." Shouldering his way past the captain he exited the locker room. Misato let out a long sigh as she rubbed her temples. "I could have handled that a lot better." She muttered to herself. 'Man I need a drink.'

* * *

Misato was nursing her fourth beer in a half hours time trying her hardest to drown out her thoughts with the alcohol. She was interrupted by the screeching of a bar stool as someone sat down next to her. Already smelling cheap perfume and cigarette smoke she groaned out loud as her new companion sat down. "What do you want Rits? Right now isn't really a great time for me."

Ritsuko scoffed at her friends greeting. "Trouble in paradise I take it? I hear that Shinji is leaving Nerv, I don't know what you told him but he did not take it very well." Her question was met with silence as Misato tried to bury her head in her arms. "I didn't mean to be so hard on him, I was just angry that he disobeyed me and almost got himself killed."

For the briefest of moments Ritsuko felt pity for her old friend, "You have to remember that he isn't a soldier he had no idea what he was getting into when he first came here." The bottle blond pulled out a cigarette and lit it. "When it comes down to it he is just a kid who got thrown into a war that he has no idea how to fight." She took a long drag before continuing. "He is probably scared to death and just needs someone to let him know that he isn't alone."

All of the times she had spent alone when she was younger came rushing back to her after listening to her friend talk. She knew how frightening it could be feeling like there wasn't anyone that understood or that would be there for you. Ritsuko was right and she felt ashamed at how she treated Shinji after the battle.

Ritsuko was startled as the purple haired captain jumped to her feet only swaying slightly from intoxication. She turned quickly and began to walk away briskly bumping into tables and chairs as she did so. Stopping at the bars exit she turned back to the stunned Ritsuko, "Thanks Rits I don't know what I would do without you." and with that she was gone.

After waiting several minutes to make sure that Misato was not coming back, she pulled out her cell phone and hit the send key. The phone rang twice before her call was answered. "It's done she is on her way right now to stop him from leaving." She was greeted only with silence, but she knew the person on the other end was listening carefully. "Are you sure about this? Pushing them this fast might not turn out so well in the end." Her question was answered by the sound of the phone call being cut off from the other end.

* * *

Fuyutsuki sat across from the commander of Nerv Gendo Ikari. There were times when he briefly wondered how he came to be in his current situation. In the end it always came back to his once-pupule, Yui Ikari. At one point he believed that he was in love with his student, but with time he realized that his love was for that of a daughter.

The professor had never married, he was always too busy with work and studying to ever find a woman for his life. To this end he never had children either, but when he met the young Ikari girl she was everything he would ever want in a daughter. Her brilliance amazed him and her kindness touched his heart. The day she was absorbed into the Eva was the darkest in his life. Today was one of the many days that he wondered if they were doing the right thing, if this is what Yui would want.

"How is the progress on the dual entry plug system?" Gendo asked while breaking the heavy silence in the process. "The project is still on schedule and it should be finished on time." Fuyutsuki reported. "And what is the status of the first child?" The second in command took a deep breath, "The first child is healing well, but it will be some time before she will be combat ready again." He paused before continuing unsure if he should even ask the question on his mind, "Do you think there will be any issues with the new pilot?"

Gendo's eyes flickered ever so slightly at his second in commands question. "There should be no issue with the pilot or with the Eva if that is where your concern lies." Fuyutsuki flinched at the commanders scathing tone, "Yes but what of.." Gendo silenced the old professor with a quick hand gesture. "Everything will go according to plan, we have gone to great lengths to see that they do, now if you have no further concerns I have other business to attend to."

Not wanting to be in Gendo's presence longer than necessary Fuyutsuki stood from his chair and began to walk away. As he neared the exit his thoughts grew heavier and heavier. 'Yui if we ever do meet I hope that you believe that what we are doing is right.' After leaving the commanders chambers he made his way home to fall asleep thinking of the daughter he never had.

* * *

See you next time!


End file.
